SYNE1 | OmnibusX

I. Expression across cell types

Name	Number of supported studies	Average coverage
endothelial cell	36 studies	50% ± 20%	Explore
natural killer cell	33 studies	41% ± 17%	Explore
fibroblast	27 studies	37% ± 16%	Explore
smooth muscle cell	23 studies	38% ± 14%	Explore
pericyte	21 studies	31% ± 13%	Explore
CD8-positive, alpha-beta T cell	20 studies	32% ± 13%	Explore
ciliated cell	19 studies	63% ± 18%	Explore
endothelial cell of lymphatic vessel	19 studies	42% ± 21%	Explore
astrocyte	19 studies	55% ± 22%	Explore
T cell	17 studies	29% ± 13%	Explore
mature NK T cell	16 studies	31% ± 11%	Explore
CD16-positive, CD56-dim natural killer cell, human	15 studies	49% ± 13%	Explore
oligodendrocyte precursor cell	15 studies	53% ± 17%	Explore
CD16-negative, CD56-bright natural killer cell, human	14 studies	34% ± 10%	Explore
effector memory CD8-positive, alpha-beta T cell	13 studies	32% ± 12%	Explore
gamma-delta T cell	13 studies	33% ± 14%	Explore
capillary endothelial cell	13 studies	39% ± 17%	Explore
type I pneumocyte	12 studies	40% ± 17%	Explore
glutamatergic neuron	12 studies	76% ± 19%	Explore
oligodendrocyte	12 studies	33% ± 15%	Explore
mucosal invariant T cell	12 studies	28% ± 8%	Explore
regulatory T cell	12 studies	20% ± 2%	Explore
type II pneumocyte	11 studies	51% ± 21%	Explore
CD8-positive, alpha-beta memory T cell	11 studies	35% ± 13%	Explore
GABAergic neuron	11 studies	65% ± 24%	Explore
CD4-positive, alpha-beta T cell	11 studies	25% ± 8%	Explore
myofibroblast cell	9 studies	29% ± 10%	Explore
microglial cell	9 studies	35% ± 19%	Explore
mesothelial cell	9 studies	47% ± 17%	Explore
epithelial cell	8 studies	37% ± 23%	Explore
amacrine cell	8 studies	50% ± 16%	Explore
retinal rod cell	7 studies	25% ± 7%	Explore
macrophage	7 studies	35% ± 11%	Explore
retinal ganglion cell	7 studies	45% ± 25%	Explore
retinal cone cell	7 studies	43% ± 10%	Explore
adipocyte	7 studies	31% ± 10%	Explore
effector memory CD8-positive, alpha-beta T cell, terminally differentiated	6 studies	38% ± 10%	Explore
CD4-positive, alpha-beta memory T cell	6 studies	23% ± 4%	Explore
naive thymus-derived CD8-positive, alpha-beta T cell	6 studies	24% ± 5%	Explore
naive thymus-derived CD4-positive, alpha-beta T cell	6 studies	21% ± 7%	Explore
neuron	6 studies	47% ± 15%	Explore
interneuron	6 studies	67% ± 26%	Explore
retina horizontal cell	6 studies	54% ± 19%	Explore
endothelial cell of artery	6 studies	26% ± 8%	Explore
endothelial cell of vascular tree	6 studies	46% ± 16%	Explore
effector CD8-positive, alpha-beta T cell	5 studies	30% ± 10%	Explore
retinal bipolar neuron	5 studies	70% ± 18%	Explore
ON-bipolar cell	5 studies	57% ± 25%	Explore
cardiac muscle cell	5 studies	52% ± 14%	Explore
vein endothelial cell	5 studies	41% ± 24%	Explore
lymphocyte	5 studies	42% ± 12%	Explore
exhausted T cell	4 studies	30% ± 11%	Explore
leukocyte	4 studies	30% ± 14%	Explore
glomerular endothelial cell	4 studies	82% ± 5%	Explore
differentiation-committed oligodendrocyte precursor	4 studies	50% ± 14%	Explore
glial cell	4 studies	30% ± 11%	Explore
granule cell	4 studies	77% ± 20%	Explore
OFF-bipolar cell	4 studies	40% ± 17%	Explore
T follicular helper cell	4 studies	18% ± 2%	Explore
innate lymphoid cell	4 studies	33% ± 10%	Explore
connective tissue cell	4 studies	38% ± 11%	Explore
club cell	4 studies	27% ± 9%	Explore
monocyte	4 studies	24% ± 7%	Explore
kidney loop of Henle epithelial cell	4 studies	30% ± 6%	Explore
hepatic stellate cell	3 studies	37% ± 15%	Explore
GABAergic interneuron	3 studies	78% ± 6%	Explore
progenitor cell	3 studies	35% ± 11%	Explore
B cell	3 studies	27% ± 7%	Explore
plasma cell	3 studies	38% ± 8%	Explore
endocardial cell	3 studies	38% ± 16%	Explore
GABAergic amacrine cell	3 studies	55% ± 20%	Explore
glycinergic amacrine cell	3 studies	48% ± 12%	Explore
rod bipolar cell	3 studies	89% ± 8%	Explore
hepatocyte	3 studies	51% ± 22%	Explore
muscle cell	3 studies	43% ± 29%	Explore
effector memory CD4-positive, alpha-beta T cell	3 studies	21% ± 6%	Explore
ependymal cell	3 studies	83% ± 2%	Explore
adventitial cell	3 studies	37% ± 9%	Explore
chondrocyte	3 studies	38% ± 17%	Explore
basal cell	3 studies	42% ± 21%	Explore
parietal epithelial cell	3 studies	81% ± 13%	Explore
renal principal cell	3 studies	39% ± 10%	Explore

II. Expression across tissues

Name	Number of supported studies	Average coverage
brain	18 studies	54% ± 22%	Explore
peripheral blood	14 studies	21% ± 5%	Explore
lung	12 studies	28% ± 12%	Explore
eye	9 studies	35% ± 12%	Explore
kidney	6 studies	30% ± 11%	Explore
heart	5 studies	41% ± 14%	Explore
adipose	4 studies	30% ± 10%	Explore
bone marrow	3 studies	24% ± 6%	Explore
uterus	3 studies	25% ± 10%	Explore
liver	3 studies	28% ± 5%	Explore

Tissue	GTEx Coverage	GTEx Average TPM	GTEx Number of samples	TCGA Coverage	TCGA Average TPM	TCGA Number of samples
brain	100%	20097.88	2634 / 2642	97%	10.78	683 / 705
kidney	100%	13885.63	89 / 89	89%	8.72	799 / 901
thymus	100%	21395.99	653 / 653	86%	6.91	522 / 605
adrenal gland	99%	8059.67	256 / 258	85%	7.22	196 / 230
breast	100%	9770.56	458 / 459	78%	3.85	869 / 1118
prostate	99%	10078.23	243 / 245	76%	4.20	383 / 502
skin	99%	7859.05	1783 / 1809	75%	3.61	355 / 472
lung	100%	17501.94	578 / 578	64%	4.65	739 / 1155
pancreas	87%	3754.74	285 / 328	77%	4.12	137 / 178
stomach	98%	7909.43	351 / 359	41%	2.29	116 / 286
bladder	100%	9149.00	21 / 21	29%	1.34	148 / 504
uterus	99%	15495.80	168 / 170	27%	2.13	126 / 459
esophagus	75%	7348.55	1090 / 1445	40%	1.91	74 / 183
ovary	100%	28083.48	180 / 180	13%	0.43	55 / 430
intestine	88%	7919.44	848 / 966	24%	1.15	129 / 527
spleen	100%	16253.12	241 / 241	0%	0	0 / 0
blood vessel	100%	18596.05	1334 / 1335	0%	0	0 / 0
adipose	100%	9559.41	1199 / 1204	0%	0	0 / 0
heart	99%	9079.21	851 / 861	0%	0	0 / 0
lymph node	0%	0	0 / 0	93%	5.91	27 / 29
muscle	84%	4493.20	675 / 803	0%	0	0 / 0
liver	54%	1812.02	123 / 226	23%	0.75	93 / 406
peripheral blood	77%	3996.79	718 / 929	0%	0	0 / 0
eye	0%	0	0 / 0	65%	3.31	52 / 80
tonsil	0%	0	0 / 0	42%	2.74	19 / 45
abdomen	0%	0	0 / 0	0%	0	0 / 0
bone marrow	0%	0	0 / 0	0%	0	0 / 0
diaphragm	0%	0	0 / 0	0%	0	0 / 0
gingiva	0%	0	0 / 0	0%	0	0 / 0
nasal cavity	0%	0	0 / 0	0%	0	0 / 0
nasopharynx	0%	0	0 / 0	0%	0	0 / 0
nose	0%	0	0 / 0	0%	0	0 / 0
placenta	0%	0	0 / 0	0%	0	0 / 0
spinal column	0%	0	0 / 0	0%	0	0 / 0
ureter	0%	0	0 / 0	0%	0	0 / 1

III. Associated gene sets

GO_0007283	Biological process	spermatogenesis
GO_0061886	Biological process	negative regulation of mini excitatory postsynaptic potential
GO_0048814	Biological process	regulation of dendrite morphogenesis
GO_0042692	Biological process	muscle cell differentiation
GO_0055007	Biological process	cardiac muscle cell differentiation
GO_1903353	Biological process	regulation of nucleus organization
GO_0048260	Biological process	positive regulation of receptor-mediated endocytosis
GO_0090292	Biological process	nuclear matrix anchoring at nuclear membrane
GO_0006997	Biological process	nucleus organization
GO_0002053	Biological process	positive regulation of mesenchymal cell proliferation
GO_0007030	Biological process	Golgi organization
GO_0099149	Biological process	regulation of postsynaptic neurotransmitter receptor internalization
GO_0009416	Biological process	response to light stimulus
GO_2001054	Biological process	negative regulation of mesenchymal cell apoptotic process
GO_0005730	Cellular component	nucleolus
GO_0030496	Cellular component	midbody
GO_0005856	Cellular component	cytoskeleton
GO_0048471	Cellular component	perinuclear region of cytoplasm
GO_0016020	Cellular component	membrane
GO_0005654	Cellular component	nucleoplasm
GO_0005794	Cellular component	Golgi apparatus
GO_0005635	Cellular component	nuclear envelope
GO_0005640	Cellular component	nuclear outer membrane
GO_0000932	Cellular component	P-body
GO_0034993	Cellular component	meiotic nuclear membrane microtubule tethering complex
GO_0030017	Cellular component	sarcomere
GO_0005737	Cellular component	cytoplasm
GO_0045211	Cellular component	postsynaptic membrane
GO_0044327	Cellular component	dendritic spine head
GO_0031965	Cellular component	nuclear membrane
GO_0005634	Cellular component	nucleus
GO_0019899	Molecular function	enzyme binding
GO_0042803	Molecular function	protein homodimerization activity
GO_0051015	Molecular function	actin filament binding
GO_0005102	Molecular function	signaling receptor binding
GO_0005521	Molecular function	lamin binding
GO_0003723	Molecular function	RNA binding
GO_0005515	Molecular function	protein binding
GO_0003779	Molecular function	actin binding
GO_0140444	Molecular function	cytoskeleton-nuclear membrane anchor activity

IV. Literature review

[source]

Gene name	SYNE1
Protein name	Synaptic nuclear envelope protein 1 Nesprin-1 (Spectrin repeat containing nuclear envelope protein 1) Nesprin-1 Spectrin-like protein of the nuclear envelope and Golgi Nesprin-1 (Enaptin) (KASH domain-containing protein 1) (KASH1) (Myocyte nuclear envelope protein 1) (Myne-1) (Nuclear envelope spectrin repeat protein 1) (Synaptic nuclear envelope protein 1) (Syne-1) SYNE1 protein Spectrin repeat containing nuclear envelope protein 1 Spectrin repeat containing nuclear envelope protein 1 (cDNA, FLJ79000, highly similar to Nesprin-1)
Synonyms	KIAA1262 KIAA0796 KIAA1756 C6orf98 MYNE1
Description	FUNCTION: Multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain the subcellular spatial organization. As a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex involved in the connection between the nuclear lamina and the cytoskeleton. The nucleocytoplasmic interactions established by the LINC complex play an important role in the transmission of mechanical forces across the nuclear envelope and in nuclear movement and positioning. May be involved in nucleus-centrosome attachment and nuclear migration in neural progenitors implicating LINC complex association with SUN1/2 and probably association with cytoplasmic dynein-dynactin motor complexes; SYNE1 and SYNE2 may act redundantly. Required for centrosome migration to the apical cell surface during early ciliogenesis. May be involved in nuclear remodeling during sperm head formation in spermatogenesis; a probable SUN3:SYNE1/KASH1 LINC complex may tether spermatid nuclei to posterior cytoskeletal structures such as the manchette. .
Accessions	ENST00000535896.7 A0A5F9ZHB2 ENST00000536990.5 ENST00000367251.7 ENST00000540663.5 ENST00000367253.8 [Q8NF91-6] ENST00000537033.1 I6WZ08 H0YGD3 ENST00000673173.1 ENST00000671915.1 F5H4Q0 A0A5F9ZH86 ENST00000367257.8 I6WZ14 A0A5F9ZI52 Q8NF91 F8WAI0 A0A5F9ZHI3 ENST00000672154.1 B7Z9Y6 ENST00000537750.5 H0Y325 ENST00000454018.7 ENST00000610489.2 F5H422 H0Y326 A0A1Z2R910 F5GYQ7 H0YFT4 ENST00000354674.5 Q7RTM4 Q5JV20 F5GZ83 ENST00000423061.6 E9PEL9 ENST00000673281.1 ENST00000673163.1 A7E2D5 A0A0C4DH48 ENST00000672122.1 ENST00000539504.5 ENST00000466159.6 F5H6R8 ENST00000413186.6 [Q8NF91-5] A0A5F9ZH87 I6XTI3 ENST00000367255.10 [Q8NF91-1] F5GXQ8 ENST00000469439.1 ENST00000673451.1 ENST00000495090.6 Q5BKU8 A0A5F9ZHD7 A0A5F9ZHE1 A0A0C4DG40 A0A5F9ZH00 I6XKI8 A0A5F9ZHR3 ENST00000367248.7 ENST00000672169.1 I6WNA2 I6XKJ3 ENST00000474655.6

SYNE1 report

I. Expression across cell types

II. Expression across tissues

III. Associated gene sets

IV. Literature review